Mr Portillo denies the allegations
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Guatemala has ordered the arrest of former President Alfonso Portillo on corruption charges, a judge in the Central American country has confirmed.
Mr Portillo fled to Mexico last year losing his legal immunity in Guatemala.
Judge Victor Hugo Rios said prosecutors would now decide whether to ask for Mr Portillo's extradition.
Mr Portillo is wanted over the disappearance of $15.7m (£9m) earmarked for the defence ministry. He has denied all the allegations.
"Yesterday (Monday), an arrest warrant was issued based on investigations by the public prosecutor's office," the judge said at a news conference in the capital, Guatemala City.
It is one of many corruption cases that emerged during Mr Portillo's term in office from 2000 to 2004.
The former president has said he fled because he could not get a fair trial in Guatemala.